Abstract

Multiple algorithms have been developed for the purpose of calling single nucleotide
polymorphisms (SNPs) from Affymetrix microarrays. We extend and validate the algorithm
CRLMM, which incorporates HapMap information within an empirical Bayes framework.
We find CRLMM to be more accurate than the Affymetrix default programs (BRLMM and
Birdseed). Also, we tie our call confidence metric to percent accuracy. We intend
that our validation datasets and methods, refered to as SNPaffycomp, serve as standard
benchmarks for future SNP calling algorithms.